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Improving pre-built DeepVariant binaries for conda packages
See original GitHub issueHi all; Thanks for all the help getting an initial conda package in place for DeepVariant (#9) through bioconda.
I wanted to follow up with some suggestions that would help make the pre-built binaries more portable as part of this process, in order of helpfulness for portability:
- Currently the binaries need a recent kernel with GLIBC > 2.23 due to pre-built htslib and other libraries. Would it be possible to build the DeepVariant libraries on an older machine to allow a wider range of system support? We build on CentOS 6 in conda to provide wider compatibility.
- main.py in the zip files hardcodes python to use
/usr/bin/python. Would it be possible to generalize this by using the python that the zip file gets called with (sys.executable)? I currently patch this in the conda build: https://github.com/bioconda/bioconda-recipes/blob/0a2d467d63d011015efeef4b644e985297b6b271/recipes/deepvariant/build.sh#L22 - This is currently built against numpy 1.13 and ideally we’d want to sync with CONDA_NPY (1.12: https://github.com/bioconda/bioconda-recipes/blob/0a2d467d63d011015efeef4b644e985297b6b271/scripts/env_matrix.yml#L9). I believe building against 1.12 would make it forward compatible.
An alternative to points 1 and 3 is making it easier to build DeepVariant as part of the conda build process. The major blocker here is the clif dependency which is difficult to build and the pre-built binaries require unpacking into /usr. If we could make this relocatable and easier to install globally we could build with portable binaries and adjustable numpy as part of the bioconda preparation process.
Thanks again for all the help.
Issue Analytics
- State:
- Created 6 years ago
- Comments:41
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We understand that building CLIF is a high tall for our users and putting efforts to make it easier.
Hi all, I know that this was not fully resolved, but by having it open forever also doesn’t seen very effective. I’m going to close it for now. But please do feel free to comment here. I will continue to read and reply anything here. If there are suggestions on how to re-engage this effort, also feel to let me know.